Back to Multiple platform build/check report for BioC 3.7
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

BUILD report for genphen on malbec2

This page was generated on 2018-10-17 08:28:45 -0400 (Wed, 17 Oct 2018).

Package 603/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genphen 1.8.0
Simo Kitanovski
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/genphen
Branch: RELEASE_3_7
Last Commit: fdf75eb
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genphen
Version: 1.8.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data genphen
StartedAt: 2018-10-15 20:59:07 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 20:59:44 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 37.1 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data genphen
###
##############################################################################
##############################################################################


* checking for file ‘genphen/DESCRIPTION’ ... OK
* preparing ‘genphen’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: genphen
Loading required package: e1071
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: rstan
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.17.4, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Loading required package: ranger
Loading required package: foreach
Loading required package: doParallel
Loading required package: iterators
Loading required package: knitr
Loading required package: ggrepel
Loading required package: reshape2
Loading required package: ape

Attaching package: ‘ape’

The following object is masked from ‘package:Biostrings’:

    complement

Loading required package: xtable
Warning in stan_model(file = f.pkg, model_name = "model") :
  StanHeaders version is ahead of rstan version; update to latest rstan
Warning in system(cmd, intern = !verbose) :
  running command '/home/biocbuild/bbs-3.7-bioc/R/bin/R CMD SHLIB file7c4254d85d58.cpp 2> file7c4254d85d58.cpp.err.txt' had status 1

Error: processing vignette 'genphenManual.Rnw' failed with diagnostics:
 chunk 1 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/config.hpp:39:0,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/BH/include/boost/math/tools/config.hpp:13,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math/rev/core/var.hpp:7,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:12,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/biocbuild/bbs-3.7-bioc/R/library/StanHeaders/include/stan/math.hpp:4,
                 from /home/biocbuild/bbs-3.7
Execution halted